FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 66QNZ

Calculation Name: 4PVC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PVC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12068

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 342
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5411568.435079
FMO2-HF: Nuclear repulsion 5278030.544489
FMO2-HF: Total energy -133537.89059
FMO2-MP2: Total energy -133929.130242


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-23.711-16.34712.573-5.914-14.0220.001
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.037
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3VAL0-0.0040.0073.252-4.840-2.5200.131-1.033-1.417-0.002
4A4PHE00.0320.0034.9970.5880.647-0.001-0.005-0.0530.000
5A5VAL00.0140.0028.3100.0470.0470.0000.0000.0000.000
6A6SER00.025-0.01311.2420.0660.0660.0000.0000.0000.000
7A7GLY0-0.022-0.00614.5140.0350.0350.0000.0000.0000.000
8A8ALA00.0340.00614.1920.0220.0220.0000.0000.0000.000
9A9ASN00.007-0.00315.9640.0280.0280.0000.0000.0000.000
10A10GLY0-0.0050.00418.9650.0000.0000.0000.0000.0000.000
11A11PHE0-0.005-0.01219.5440.0230.0230.0000.0000.0000.000
12A12ILE00.0610.01816.7330.0230.0230.0000.0000.0000.000
13A13ALA00.0060.01215.3030.0410.0410.0000.0000.0000.000
14A14GLN00.014-0.00114.8220.0720.0720.0000.0000.0000.000
15A15HIS00.009-0.01216.0090.0810.0810.0000.0000.0000.000
16A16ILE0-0.031-0.00310.8110.0600.0600.0000.0000.0000.000
17A17VAL0-0.010-0.00611.2490.1120.1120.0000.0000.0000.000
18A18ASP-1-0.853-0.94511.6640.6400.6400.0000.0000.0000.000
19A19LEU0-0.049-0.03012.2360.0830.0830.0000.0000.0000.000
20A20LEU0-0.0050.0056.1810.1300.1300.0000.0000.0000.000
21A21LEU0-0.026-0.0147.8990.3150.3150.0000.0000.0000.000
22A22LYS10.8590.9439.842-0.449-0.4490.0000.0000.0000.000
23A23GLU-1-0.893-0.9418.1961.1181.1180.0000.0000.0000.000
24A24ASP-1-0.930-0.9607.3151.7451.7450.0000.0000.0000.000
25A25TYR0-0.054-0.0212.439-1.772-0.2792.645-1.039-3.098-0.002
26A26LYS10.8720.9363.104-12.827-10.6770.155-1.090-1.2150.011
27A27VAL00.0070.0045.180-0.828-0.841-0.001-0.0080.0220.000
28A28ILE00.0270.0227.9360.0140.0140.0000.0000.0000.000
29A29GLY00.0460.01910.325-0.127-0.1270.0000.0000.0000.000
30A30SER00.0280.01813.060-0.022-0.0220.0000.0000.0000.000
31A31ALA00.0220.00416.1910.0260.0260.0000.0000.0000.000
32A32ARG10.9120.96719.8120.0080.0080.0000.0000.0000.000
33A33SER0-0.005-0.00923.056-0.005-0.0050.0000.0000.0000.000
34A34GLN00.0690.01422.522-0.011-0.0110.0000.0000.0000.000
35A35GLU-1-0.885-0.92823.9630.0670.0670.0000.0000.0000.000
36A36LYS10.8550.92022.916-0.023-0.0230.0000.0000.0000.000
37A37ALA00.0170.01219.8230.0180.0180.0000.0000.0000.000
38A38GLU-1-0.846-0.93420.1640.1530.1530.0000.0000.0000.000
39A39ASN00.0140.00422.4370.0250.0250.0000.0000.0000.000
40A40LEU0-0.040-0.01516.7380.0150.0150.0000.0000.0000.000
41A41THR0-0.026-0.02616.4460.0350.0350.0000.0000.0000.000
42A42GLU-1-0.911-0.93918.5630.2350.2350.0000.0000.0000.000
43A43ALA0-0.069-0.03020.8350.0170.0170.0000.0000.0000.000
44A44PHE0-0.027-0.02415.6900.0160.0160.0000.0000.0000.000
45A45GLY0-0.028-0.00817.2490.0650.0650.0000.0000.0000.000
46A46ASN0-0.054-0.03118.3410.0060.0060.0000.0000.0000.000
47A47ASN00.0420.02512.4730.1100.1100.0000.0000.0000.000
48A48PRO00.0670.03013.5720.0200.0200.0000.0000.0000.000
49A49LYS10.8360.9256.735-2.610-2.6100.0000.0000.0000.000
50A50PHE0-0.036-0.0179.0090.1950.1950.0000.0000.0000.000
51A51SER0-0.0070.01111.365-0.133-0.1330.0000.0000.0000.000
52A52MET0-0.039-0.00513.247-0.045-0.0450.0000.0000.0000.000
53A53GLU-1-0.858-0.93214.685-0.085-0.0850.0000.0000.0000.000
54A54VAL0-0.021-0.01517.1290.0040.0040.0000.0000.0000.000
55A55VAL00.003-0.00217.496-0.023-0.0230.0000.0000.0000.000
56A56PRO0-0.046-0.02320.6450.0080.0080.0000.0000.0000.000
57A57ASP-1-0.859-0.93323.656-0.092-0.0920.0000.0000.0000.000
58A58ILE0-0.025-0.01719.908-0.012-0.0120.0000.0000.0000.000
59A59SER0-0.024-0.00722.057-0.021-0.0210.0000.0000.0000.000
60A60LYS10.9220.97524.7320.0950.0950.0000.0000.0000.000
61A61LEU00.020-0.00923.111-0.016-0.0160.0000.0000.0000.000
62A62ASP-1-0.891-0.93021.895-0.209-0.2090.0000.0000.0000.000
63A63ALA0-0.047-0.01320.735-0.008-0.0080.0000.0000.0000.000
64A64PHE0-0.018-0.03215.4990.0170.0170.0000.0000.0000.000
65A65ASP-1-0.785-0.88216.239-0.396-0.3960.0000.0000.0000.000
66A66HIS0-0.053-0.02517.382-0.022-0.0220.0000.0000.0000.000
67A67VAL00.0240.01512.2440.0030.0030.0000.0000.0000.000
68A68PHE00.0390.0039.619-0.056-0.0560.0000.0000.0000.000
69A69GLN0-0.0240.00313.430-0.065-0.0650.0000.0000.0000.000
70A70LYS10.8620.93614.4390.0770.0770.0000.0000.0000.000
71A71HIS00.0020.00410.0600.0290.0290.0000.0000.0000.000
72A72GLY00.0550.0389.496-0.291-0.2910.0000.0000.0000.000
73A73LYS10.9420.9789.1230.1890.1890.0000.0000.0000.000
74A74ASP-1-0.928-0.9474.783-0.866-0.808-0.001-0.011-0.0460.000
75A75ILE0-0.0240.0094.680-1.605-1.611-0.001-0.0370.0430.000
76A76LYS10.9660.9931.9903.6763.1086.825-1.726-4.531-0.002
77A77ILE0-0.0090.0082.555-0.4670.3292.747-0.639-2.904-0.003
78A78VAL00.0110.0064.8200.1040.123-0.001-0.007-0.0100.000
79A79LEU0-0.015-0.0067.7680.1640.1640.0000.0000.0000.000
80A80HIS00.0200.01710.6400.0190.0190.0000.0000.0000.000
81A81THR00.011-0.01813.9620.0470.0470.0000.0000.0000.000
82A82ALA0-0.059-0.01816.4370.0280.0280.0000.0000.0000.000
83A83SER00.007-0.01018.856-0.022-0.0220.0000.0000.0000.000
84A84PRO00.0120.00922.3240.0080.0080.0000.0000.0000.000
85A85PHE0-0.045-0.02325.1890.0160.0160.0000.0000.0000.000
86A86CYS00.0470.05227.209-0.002-0.0020.0000.0000.0000.000
87A87PHE0-0.084-0.06630.285-0.006-0.0060.0000.0000.0000.000
88A88ASP-1-0.805-0.93232.819-0.031-0.0310.0000.0000.0000.000
89A89ILE0-0.035-0.02436.226-0.004-0.0040.0000.0000.0000.000
90A90THR0-0.0300.00438.5890.0010.0010.0000.0000.0000.000
91A91ASP-1-0.890-0.94238.858-0.065-0.0650.0000.0000.0000.000
92A92SER00.0400.01136.178-0.003-0.0030.0000.0000.0000.000
93A93GLU-1-0.859-0.92734.575-0.092-0.0920.0000.0000.0000.000
94A94ARG10.8690.93533.7940.0500.0500.0000.0000.0000.000
95A95ASP-1-0.834-0.91933.402-0.064-0.0640.0000.0000.0000.000
96A96LEU0-0.050-0.03430.3070.0030.0030.0000.0000.0000.000
97A97LEU0-0.053-0.03129.861-0.008-0.0080.0000.0000.0000.000
98A98ILE00.0150.01129.306-0.013-0.0130.0000.0000.0000.000
99A99PRO00.0050.00227.804-0.017-0.0170.0000.0000.0000.000
100A100ALA0-0.0060.00225.419-0.014-0.0140.0000.0000.0000.000
101A101VAL0-0.0080.00224.148-0.018-0.0180.0000.0000.0000.000
102A102ASN00.009-0.00923.887-0.035-0.0350.0000.0000.0000.000
103A103GLY0-0.010-0.00122.083-0.020-0.0200.0000.0000.0000.000
104A104VAL0-0.0140.00918.949-0.018-0.0180.0000.0000.0000.000
105A105LYS10.9850.97319.0930.1840.1840.0000.0000.0000.000
106A106GLY00.0170.02420.300-0.029-0.0290.0000.0000.0000.000
107A107ILE00.0030.00113.035-0.032-0.0320.0000.0000.0000.000
108A108LEU00.0060.01314.706-0.082-0.0820.0000.0000.0000.000
109A109HIS00.0210.00616.478-0.066-0.0660.0000.0000.0000.000
110A110SER0-0.030-0.04216.003-0.006-0.0060.0000.0000.0000.000
111A111ILE0-0.047-0.01311.429-0.044-0.0440.0000.0000.0000.000
112A112LYS10.8820.93414.0310.3420.3420.0000.0000.0000.000
113A113LYS10.8710.94416.2500.3190.3190.0000.0000.0000.000
114A114TYR0-0.034-0.03015.1580.0530.0530.0000.0000.0000.000
115A115ALA0-0.011-0.00210.366-0.027-0.0270.0000.0000.0000.000
116A116ALA00.0370.03311.020-0.180-0.1800.0000.0000.0000.000
117A117ASP-1-0.940-0.96511.706-1.046-1.0460.0000.0000.0000.000
118A118SER0-0.050-0.0507.602-0.046-0.0460.0000.0000.0000.000
119A119VAL0-0.029-0.0136.126-0.814-0.8140.0000.0000.0000.000
120A120GLU-1-0.935-0.9783.759-5.206-4.5880.019-0.206-0.432-0.001
121A121ARG10.8190.9095.5741.3351.3350.0000.0000.0000.000
122A122VAL00.0210.0177.140-0.074-0.0740.0000.0000.0000.000
123A123VAL0-0.009-0.0089.5930.1040.1040.0000.0000.0000.000
124A124LEU0-0.006-0.00312.0740.0020.0020.0000.0000.0000.000
125A125THR0-0.019-0.02815.6530.0310.0310.0000.0000.0000.000
126A126SER0-0.060-0.05117.755-0.004-0.0040.0000.0000.0000.000
127A127SER0-0.022-0.03621.1270.0230.0230.0000.0000.0000.000
128A128TYR0-0.008-0.00524.237-0.013-0.0130.0000.0000.0000.000
129A129ALA00.0310.01426.767-0.004-0.0040.0000.0000.0000.000
130A130ALA00.0200.00825.245-0.002-0.0020.0000.0000.0000.000
131A131VAL0-0.087-0.02925.832-0.008-0.0080.0000.0000.0000.000
132A132PHE0-0.027-0.00428.4050.0000.0000.0000.0000.0000.000
133A133ASP-1-0.786-0.91231.904-0.054-0.0540.0000.0000.0000.000
134A134MET00.0100.00735.4050.0040.0040.0000.0000.0000.000
135A135ALA00.000-0.00336.7900.0050.0050.0000.0000.0000.000
136A136LYS10.8900.94238.3760.0460.0460.0000.0000.0000.000
137A137GLU-1-0.739-0.85934.021-0.016-0.0160.0000.0000.0000.000
138A138ASN00.007-0.00537.8300.0060.0060.0000.0000.0000.000
139A139ASP-1-0.857-0.91140.789-0.021-0.0210.0000.0000.0000.000
140A140LYS10.9740.97040.3550.0030.0030.0000.0000.0000.000
141A141SER0-0.128-0.05540.547-0.001-0.0010.0000.0000.0000.000
142A142LEU00.0020.00838.120-0.004-0.0040.0000.0000.0000.000
143A143THR0-0.018-0.02232.9530.0060.0060.0000.0000.0000.000
144A144PHE00.0010.01131.083-0.006-0.0060.0000.0000.0000.000
145A145ASN00.0390.00628.1090.0020.0020.0000.0000.0000.000
146A146GLU-1-0.751-0.87222.628-0.057-0.0570.0000.0000.0000.000
147A147GLU-1-0.976-0.97624.927-0.130-0.1300.0000.0000.0000.000
148A148SER0-0.043-0.00327.1720.0020.0020.0000.0000.0000.000
149A149TRP00.0170.01223.479-0.001-0.0010.0000.0000.0000.000
150A150ASN00.0140.01629.5360.0050.0050.0000.0000.0000.000
151A151PRO00.0240.01131.786-0.009-0.0090.0000.0000.0000.000
152A152ALA0-0.0240.00634.333-0.001-0.0010.0000.0000.0000.000
153A153THR00.030-0.00133.896-0.008-0.0080.0000.0000.0000.000
154A154TRP0-0.022-0.02430.3920.0000.0000.0000.0000.0000.000
155A155GLU-1-0.860-0.93435.298-0.079-0.0790.0000.0000.0000.000
156A156SER0-0.0040.00138.4430.0030.0030.0000.0000.0000.000
157A157CYS0-0.077-0.01335.0620.0040.0040.0000.0000.0000.000
158A158GLN0-0.010-0.02537.1900.0070.0070.0000.0000.0000.000
159A159SER0-0.042-0.00238.9820.0020.0020.0000.0000.0000.000
160A160ASP-1-0.826-0.91039.560-0.030-0.0300.0000.0000.0000.000
161A161PRO00.0530.01737.679-0.004-0.0040.0000.0000.0000.000
162A162VAL0-0.0080.00535.592-0.002-0.0020.0000.0000.0000.000
163A163ASN0-0.018-0.02934.727-0.007-0.0070.0000.0000.0000.000
164A164ALA00.0530.05034.722-0.007-0.0070.0000.0000.0000.000
165A165TYR00.0030.00127.648-0.009-0.0090.0000.0000.0000.000
166A166CYS0-0.033-0.02230.150-0.005-0.0050.0000.0000.0000.000
167A167GLY00.0400.01530.094-0.008-0.0080.0000.0000.0000.000
168A168SER0-0.053-0.03928.932-0.013-0.0130.0000.0000.0000.000
169A169LYS10.9210.95822.9280.0660.0660.0000.0000.0000.000
170A170LYS10.8120.90625.2880.0870.0870.0000.0000.0000.000
171A171PHE00.000-0.02026.085-0.016-0.0160.0000.0000.0000.000
172A172ALA00.0140.02022.995-0.016-0.0160.0000.0000.0000.000
173A173GLU-1-0.693-0.80420.506-0.175-0.1750.0000.0000.0000.000
174A174LYS10.8960.95821.6390.1300.1300.0000.0000.0000.000
175A175ALA00.0210.01223.011-0.016-0.0160.0000.0000.0000.000
176A176ALA0-0.017-0.00617.725-0.026-0.0260.0000.0000.0000.000
177A177TRP0-0.069-0.05417.061-0.053-0.0530.0000.0000.0000.000
178A178GLU-1-0.834-0.91720.224-0.216-0.2160.0000.0000.0000.000
179A179PHE0-0.0080.00216.499-0.014-0.0140.0000.0000.0000.000
180A180LEU0-0.018-0.01414.650-0.011-0.0110.0000.0000.0000.000
181A181GLU-1-1.001-1.00818.145-0.273-0.2730.0000.0000.0000.000
182A182GLU-1-0.958-0.97721.301-0.255-0.2550.0000.0000.0000.000
183A183ASN0-0.062-0.02218.8510.0110.0110.0000.0000.0000.000
184A184ARG10.9880.99317.1570.3600.3600.0000.0000.0000.000
185A185ASP-1-0.875-0.93017.128-0.442-0.4420.0000.0000.0000.000
186A186SER0-0.158-0.07518.231-0.001-0.0010.0000.0000.0000.000
187A187VAL0-0.042-0.02713.425-0.037-0.0370.0000.0000.0000.000
188A188LYS10.9520.9937.5231.9471.9470.0000.0000.0000.000
189A189PHE0-0.063-0.0239.152-0.011-0.0110.0000.0000.0000.000
190A190GLU-1-0.884-0.9399.409-0.536-0.5360.0000.0000.0000.000
191A191LEU0-0.049-0.02510.473-0.068-0.0680.0000.0000.0000.000
192A192THR0-0.044-0.03112.7140.0210.0210.0000.0000.0000.000
193A193ALA0-0.0020.02214.221-0.006-0.0060.0000.0000.0000.000
194A194VAL00.0110.00115.1040.0280.0280.0000.0000.0000.000
195A195ASN0-0.041-0.04418.015-0.010-0.0100.0000.0000.0000.000
196A196PRO0-0.0030.00220.5490.0100.0100.0000.0000.0000.000
197A197VAL0-0.0410.00223.172-0.015-0.0150.0000.0000.0000.000
198A198TYR0-0.025-0.00626.4040.0010.0010.0000.0000.0000.000
199A199VAL0-0.025-0.01022.7500.0060.0060.0000.0000.0000.000
200A200PHE00.0330.00826.005-0.003-0.0030.0000.0000.0000.000
201A201GLY00.0780.02925.5120.0110.0110.0000.0000.0000.000
202A202PRO0-0.0110.01124.208-0.008-0.0080.0000.0000.0000.000
203A203GLN00.012-0.01223.8720.0020.0020.0000.0000.0000.000
204A204MET0-0.0220.02018.3730.0030.0030.0000.0000.0000.000
205A205PHE00.0090.00018.9420.0070.0070.0000.0000.0000.000
206A206ASP-1-0.819-0.91324.3390.1620.1620.0000.0000.0000.000
207A207LYS10.8710.94124.061-0.220-0.2200.0000.0000.0000.000
208A208ASP-1-0.865-0.93924.4540.1500.1500.0000.0000.0000.000
209A209VAL00.0020.01028.140-0.014-0.0140.0000.0000.0000.000
210A210LYS10.8870.96530.624-0.087-0.0870.0000.0000.0000.000
211A211LYS10.9260.93830.717-0.077-0.0770.0000.0000.0000.000
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273A273GLN00.0000.01039.5880.0010.0010.0000.0000.0000.000
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279A279LEU0-0.047-0.02236.9610.0040.0040.0000.0000.0000.000
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293A293GLY00.0110.00847.1610.0000.0000.0000.0000.0000.000
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312A312LYS10.9260.97321.4580.1290.1290.0000.0000.0000.000
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314A314LYS10.8480.93520.267-0.024-0.0240.0000.0000.0000.000
315A315LYS10.8980.95721.4410.0490.0490.0000.0000.0000.000
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